W. Yang
@wenjiany.bsky.social
Reposted by W. Yang
Epigenetic diagnosis of acute leukemia within two hours from sample receipt 🚀
Very happy to share the results of a great collaboration between @hovestadt.bsky.social and Griffin Labs, I co-led with @sbenfatto.bsky.social, published today in @natgenet.nature.com
📄 www.nature.com/articles/s41...
🧵1/n
Very happy to share the results of a great collaboration between @hovestadt.bsky.social and Griffin Labs, I co-led with @sbenfatto.bsky.social, published today in @natgenet.nature.com
📄 www.nature.com/articles/s41...
🧵1/n
Rapid epigenomic classification of acute leukemia - Nature Genetics
The authors present a molecular classification of acute leukemia using 5-methylcytosine signatures, together with a neural network-based classifier for clinical use.
www.nature.com
September 22, 2025 at 8:41 PM
Epigenetic diagnosis of acute leukemia within two hours from sample receipt 🚀
Very happy to share the results of a great collaboration between @hovestadt.bsky.social and Griffin Labs, I co-led with @sbenfatto.bsky.social, published today in @natgenet.nature.com
📄 www.nature.com/articles/s41...
🧵1/n
Very happy to share the results of a great collaboration between @hovestadt.bsky.social and Griffin Labs, I co-led with @sbenfatto.bsky.social, published today in @natgenet.nature.com
📄 www.nature.com/articles/s41...
🧵1/n
Reposted by W. Yang
Apple is entering the protein folding arena.
SimpleFold: Folding Proteins is Simpler than You Think arxiv.org/abs/2509.18480 🧬🖥️🧪 github.com/apple/ml-sim...
SimpleFold: Folding Proteins is Simpler than You Think arxiv.org/abs/2509.18480 🧬🖥️🧪 github.com/apple/ml-sim...
September 25, 2025 at 9:02 AM
Apple is entering the protein folding arena.
SimpleFold: Folding Proteins is Simpler than You Think arxiv.org/abs/2509.18480 🧬🖥️🧪 github.com/apple/ml-sim...
SimpleFold: Folding Proteins is Simpler than You Think arxiv.org/abs/2509.18480 🧬🖥️🧪 github.com/apple/ml-sim...
Reposted by W. Yang
📢 Meet Biomni — the first general-purpose biomedical AI agent.
It automates literature review, hypothesis generation, protocol design, bioinformatics analysis, clinical decision support, and much more — scaling biomedical expertise for 100× discoveries.
biomni.stanford.edu
🧵
It automates literature review, hypothesis generation, protocol design, bioinformatics analysis, clinical decision support, and much more — scaling biomedical expertise for 100× discoveries.
biomni.stanford.edu
🧵
May 29, 2025 at 5:26 PM
📢 Meet Biomni — the first general-purpose biomedical AI agent.
It automates literature review, hypothesis generation, protocol design, bioinformatics analysis, clinical decision support, and much more — scaling biomedical expertise for 100× discoveries.
biomni.stanford.edu
🧵
It automates literature review, hypothesis generation, protocol design, bioinformatics analysis, clinical decision support, and much more — scaling biomedical expertise for 100× discoveries.
biomni.stanford.edu
🧵
Reposted by W. Yang
Excited to launch our AlphaGenome API goo.gle/3ZPUeFX along with the preprint goo.gle/45AkUyc describing and evaluating our latest DNA sequence model powering the API. Looking forward to seeing how scientists use it! @googledeepmind
June 25, 2025 at 2:29 PM
Excited to launch our AlphaGenome API goo.gle/3ZPUeFX along with the preprint goo.gle/45AkUyc describing and evaluating our latest DNA sequence model powering the API. Looking forward to seeing how scientists use it! @googledeepmind
Reposted by W. Yang
My new #math series in the New York Times, "Math Revealed," is aimed at everyone, whether you love math or not. Have a look! You can read it here for free without a subscription. www.nytimes.com/interactive/...
In Taxicab Geometry, Pi Equals 4 and Circles Aren’t Round (Gift Article)
In the world of taxicab geometry, even the Pythagorean theorem takes a back seat.
www.nytimes.com
June 9, 2025 at 10:00 AM
My new #math series in the New York Times, "Math Revealed," is aimed at everyone, whether you love math or not. Have a look! You can read it here for free without a subscription. www.nytimes.com/interactive/...
Reposted by W. Yang
Free in-person registration is open for #MLCB2025! Sept 10-11 at @nygenome.org and online at youtube.com/@mlcbconf. Paper/abstract deadline is June 1, more deets including our fantastic invited speaker lineup at mlcb.org! Please RP.
Machine Learning in Computational Biology
Youtube channel for the Machine Learning in Computational Biology conference: https://mlcb.github.io/
youtube.com
May 15, 2025 at 12:24 AM
Free in-person registration is open for #MLCB2025! Sept 10-11 at @nygenome.org and online at youtube.com/@mlcbconf. Paper/abstract deadline is June 1, more deets including our fantastic invited speaker lineup at mlcb.org! Please RP.
Reposted by W. Yang
From cell lines to full embryos, drug treatments to genetic perturbations, neuron engineering to virtual organoid screens — odds are there’s something in it for you!
Built on flow matching, CellFlow can help guide your next phenotypic screen: biorxiv.org/content/10.1101/2025.04.11.648220v1
Built on flow matching, CellFlow can help guide your next phenotypic screen: biorxiv.org/content/10.1101/2025.04.11.648220v1
April 23, 2025 at 9:26 AM
From cell lines to full embryos, drug treatments to genetic perturbations, neuron engineering to virtual organoid screens — odds are there’s something in it for you!
Built on flow matching, CellFlow can help guide your next phenotypic screen: biorxiv.org/content/10.1101/2025.04.11.648220v1
Built on flow matching, CellFlow can help guide your next phenotypic screen: biorxiv.org/content/10.1101/2025.04.11.648220v1
Reposted by W. Yang
In the history of evolution, multicellularity has evolved independently at least 50 times. But we’ve only figured that out in the past few decades. Listen to the first episode of the new season of “The Joy of Why” with hosts @stevenstrogatz.com and Janna Levin.
www.quantamagazine.org/how-did-mult...
www.quantamagazine.org/how-did-mult...
How Did Multicellular Life Evolve? | Quanta Magazine
One of the most important events in the history of life on Earth was the emergence of multicellularity. In this episode, Will Ratcliff discusses how his snowflake yeast models provide insight into wha...
www.quantamagazine.org
March 20, 2025 at 2:11 PM
In the history of evolution, multicellularity has evolved independently at least 50 times. But we’ve only figured that out in the past few decades. Listen to the first episode of the new season of “The Joy of Why” with hosts @stevenstrogatz.com and Janna Levin.
www.quantamagazine.org/how-did-mult...
www.quantamagazine.org/how-did-mult...
Reposted by W. Yang
Review: Epigenetic ageing clocks: statistical methods and emerging computational challenges https://www.nature.com/articles/s41576-024-00807-w (free: https://rdcu.be/d56ye) 🧬🖥️🧪
January 13, 2025 at 4:30 PM
Review: Epigenetic ageing clocks: statistical methods and emerging computational challenges https://www.nature.com/articles/s41576-024-00807-w (free: https://rdcu.be/d56ye) 🧬🖥️🧪
Reposted by W. Yang
A DNA language model based on multispecies alignment predicts the effects of genome-wide variants - @yun-s-song.bsky.social go.nature.com/4gWppWg
A DNA language model based on multispecies alignment predicts the effects of genome-wide variants - Nature Biotechnology
A language model predicts the effects of genetic variants in the human genome.
go.nature.com
January 2, 2025 at 4:18 PM
A DNA language model based on multispecies alignment predicts the effects of genome-wide variants - @yun-s-song.bsky.social go.nature.com/4gWppWg
Reposted by W. Yang
Latest preprint from the lab: we asked whether native RNA sequencing (using nanopore sequencing) might be a successor to traditional cDNA sequencing for biomarker discovery in blood.
Utilising Nanopore direct RNA sequencing of blood from patients with sepsis for discovery of co- and post-transcriptional disease biomarkers https://www.medrxiv.org/content/10.1101/2024.12.13.24318230v1
December 15, 2024 at 10:34 AM
Latest preprint from the lab: we asked whether native RNA sequencing (using nanopore sequencing) might be a successor to traditional cDNA sequencing for biomarker discovery in blood.
Reposted by W. Yang
'Haematological setpoints reflect a deep physiologic phenotype enabling investigation of acquired and genetic determinants of haematological regulation and its variation among healthy adults.'
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Haematological setpoints are a stable and patient-specific deep phenotype - Nature
Complete blood count indices are tightly regulated around setpoints for decades in healthy adults, and represent a deep phenotype providing opportunities for investigating differential disease risks, ...
www.nature.com
December 13, 2024 at 7:38 AM
'Haematological setpoints reflect a deep physiologic phenotype enabling investigation of acquired and genetic determinants of haematological regulation and its variation among healthy adults.'
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Nice to see more mastodon accounts showing up... Are there any starter packs for mastodon accounts over the bridge? #rstats
#rstats {dbi.table}: Database Queries Using 'data.table' Syntax
Query database tables over a 'DBI' connection using 'data.table' syntax. Attach database schemas to the search path. Automatically merge using FK constraints. Supports DuckDB!
Looks interesting! […]
Query database tables over a 'DBI' connection using 'data.table' syntax. Attach database schemas to the search path. Automatically merge using FK constraints. Supports DuckDB!
Looks interesting! […]
Original post on mastodon.social
mastodon.social
December 11, 2024 at 12:25 AM
Nice to see more mastodon accounts showing up... Are there any starter packs for mastodon accounts over the bridge? #rstats
Reposted by W. Yang
My default explanation for sudden changes in a time series is change in measurement.
So glad to see another example, sent to me by a colleague who shares my cynicism. Short, clear explanation of Liquid Chromatography-Tandem Mass Spectrometry. Which is important to the story.
So glad to see another example, sent to me by a colleague who shares my cynicism. Short, clear explanation of Liquid Chromatography-Tandem Mass Spectrometry. Which is important to the story.
Maybe it's just YOUR testosterone that's low
How the measurement tools have led us to falsely believe our T is low
eryney.substack.com
December 3, 2024 at 9:50 AM
My default explanation for sudden changes in a time series is change in measurement.
So glad to see another example, sent to me by a colleague who shares my cynicism. Short, clear explanation of Liquid Chromatography-Tandem Mass Spectrometry. Which is important to the story.
So glad to see another example, sent to me by a colleague who shares my cynicism. Short, clear explanation of Liquid Chromatography-Tandem Mass Spectrometry. Which is important to the story.
Reposted by W. Yang
Our @pydata.bsky.social tutorial with @fonnesbeck.bsky.social on Mastering #GaussianProcesses with @pymc-devs.bsky.social is now online 🥳
If you missed it live, come check it out!
Enjoy & PyMCheers 🖖
Video: www.youtube.com/watch?v=u6I5...
GitHub repo: github.com/AlexAndorra/...
If you missed it live, come check it out!
Enjoy & PyMCheers 🖖
Video: www.youtube.com/watch?v=u6I5...
GitHub repo: github.com/AlexAndorra/...
Alexandre Andorra & Christopher Fonnesbeck- Mastering Gaussian Processes with PyMC | PyData NYC 2024
YouTube video by PyData
www.youtube.com
December 2, 2024 at 4:04 PM
Our @pydata.bsky.social tutorial with @fonnesbeck.bsky.social on Mastering #GaussianProcesses with @pymc-devs.bsky.social is now online 🥳
If you missed it live, come check it out!
Enjoy & PyMCheers 🖖
Video: www.youtube.com/watch?v=u6I5...
GitHub repo: github.com/AlexAndorra/...
If you missed it live, come check it out!
Enjoy & PyMCheers 🖖
Video: www.youtube.com/watch?v=u6I5...
GitHub repo: github.com/AlexAndorra/...
Reposted by W. Yang
Imagine finding out @vincentab.bsky.social @noahgreifer.bsky.social and @andrew.heiss.phd wrote a thing and it's open access 👀
Awesome paper about {marginaleffects} R/python packages in JOSS (which needs to join Bsky)
www.jstatsoft.org/article/view...
Awesome paper about {marginaleffects} R/python packages in JOSS (which needs to join Bsky)
www.jstatsoft.org/article/view...
How to Interpret Statistical Models Using marginaleffects for R and Python by Vincent Arel-Bundock, Noah Greifer, Andrew Heiss
<p>The parameters of a statistical model can sometimes be difficult to interpret substantively, especially when that model includes nonlinear components, interactions, or transformations. Analysts who...
www.jstatsoft.org
December 1, 2024 at 10:03 PM
Imagine finding out @vincentab.bsky.social @noahgreifer.bsky.social and @andrew.heiss.phd wrote a thing and it's open access 👀
Awesome paper about {marginaleffects} R/python packages in JOSS (which needs to join Bsky)
www.jstatsoft.org/article/view...
Awesome paper about {marginaleffects} R/python packages in JOSS (which needs to join Bsky)
www.jstatsoft.org/article/view...
Reposted by W. Yang
“As a society, we need to reconsider why we are shielding our children — and ourselves — from death and dying, and what we lose when we do. We need to turn toward, rather than run from, the people who know this terrible world best: bereaved parents.”
So important 💔
www.nytimes.com/2024/11/25/o...
So important 💔
www.nytimes.com/2024/11/25/o...
Opinion | If My Dying Daughter Could Face Her Mortality, Why Couldn’t the Rest of Us?
A bereaved mother’s case against our grief-phobic culture.
www.nytimes.com
December 1, 2024 at 3:01 PM
“As a society, we need to reconsider why we are shielding our children — and ourselves — from death and dying, and what we lose when we do. We need to turn toward, rather than run from, the people who know this terrible world best: bereaved parents.”
So important 💔
www.nytimes.com/2024/11/25/o...
So important 💔
www.nytimes.com/2024/11/25/o...
Reposted by W. Yang
Timescales in Cell Biology
December 1, 2024 at 1:35 PM
Timescales in Cell Biology
Reposted by W. Yang
